Uploaded image for project: 'IGB'
  1. IGB
  2. IGBF-2860

Disable Ensembl external view

        Details

          Description

          Currently the ensembl external view does not work, regardless of the genome shown.

            Attachments

              Issue Links

              relates to

              Bug - A problem which impairs or prevents the functions of the product. IGBF-2776 Fix External View tab

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-2855 Investigate activating UCSC DAS source from External View tab

              • Major - Major loss of function.
              • Closed

              Improvement - An improvement or enhancement to an existing feature or task. IGBF-2864 Improve External View error message displayed when no genome is selected

              • Major - Major loss of function.
              • Closed

                Activity

                Descending order - Click to sort in ascending order
                Hide
                Permalink
                omarne Omkar Marne (Inactive) added a comment -

                Tested on lnux using master.sh file. The ensemble option is not visible now in the dropdown box.

                Closing the issue

                Show
                omarne Omkar Marne (Inactive) added a comment - Tested on lnux using master.sh file. The ensemble option is not visible now in the dropdown box. Closing the issue
                Hide
                Permalink
                nfreese Nowlan Freese added a comment -

                Tested on Mac using master installer.

                The Ensembl External View tab dropdown option does not appear. UCSC External View continues to work correctly.

                Closing issue.

                Show
                nfreese Nowlan Freese added a comment - Tested on Mac using master installer. The Ensembl External View tab dropdown option does not appear. UCSC External View continues to work correctly. Closing issue.
                Hide
                Permalink
                ann.loraine Ann Loraine added a comment -

                PR is submitted and merged. Master branch installers are built and ready for final testing.

                Show
                ann.loraine Ann Loraine added a comment - PR is submitted and merged. Master branch installers are built and ready for final testing.
                Hide
                Permalink
                nfreese Nowlan Freese added a comment - - edited

                Tested on Mac using branch installer.

                The ensembl external view option does not appear. UCSC external view continues to work correctly.

                Recommend pull request.

                Sidenote: I was able to debut the test file. It seems the @Ignore causes the Netbeans debugger to skip over any breakpoints in the tagged method. Need to remove the @Ignore and do a mvn clean install -DskipTests and then debug the test file.

                I also could not get the ensembl image to work. A quick search of the ensembl API was not able to find any obvious solution.

                Show
                nfreese Nowlan Freese added a comment - - edited Tested on Mac using branch installer. The ensembl external view option does not appear. UCSC external view continues to work correctly. Recommend pull request. Sidenote: I was able to debut the test file. It seems the @Ignore causes the Netbeans debugger to skip over any breakpoints in the tagged method. Need to remove the @Ignore and do a mvn clean install -DskipTests and then debug the test file. I also could not get the ensembl image to work. A quick search of the ensembl API was not able to find any obvious solution.
                Hide
                Permalink
                ann.loraine Ann Loraine added a comment -

                Removed Ensembl option from the External View interface, added new testing code, updated comments, and reduced complexity a bit.
                See branch IGBF-2860 on fork https://bitbucket.org/aloraine/integrated-genome-browser.

                Nowlan Freese - could you review?

                Show
                ann.loraine Ann Loraine added a comment - Removed Ensembl option from the External View interface, added new testing code, updated comments, and reduced complexity a bit. See branch IGBF-2860 on fork https://bitbucket.org/aloraine/integrated-genome-browser . Nowlan Freese - could you review?
                Hide
                Permalink
                ann.loraine Ann Loraine added a comment -

                Can't fix at this time because I can't figure out how to construct the URL needed to retrieve the image to be shown in the tabbed panel interface.

                Show
                ann.loraine Ann Loraine added a comment - Can't fix at this time because I can't figure out how to construct the URL needed to retrieve the image to be shown in the tabbed panel interface.

                  People

                  • Assignee:
                    ann.loraine Ann Loraine
                    Reporter:
                    ann.loraine Ann Loraine
                  • Votes:
                    0 Vote for this issue
                    Watchers:
                    3 Start watching this issue

                    Dates

                    • Created:
                      Updated:
                      Resolved: